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A common reason for the Index Status count to go down at the "update" is that an alternate version of the website is verified in Webmaster Tools. A simple way to double-check that is to do a site:-query for just your domain name (eg ), and to see which version is shown. If the www-version is shown, then that's the version where most of your data will be. If you want to be on the safe side, just verify both of them.
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Thank you +John Mueller for the this interesting info... but in my case I have a sub domain which falling down it's index status in GWT and both version of the website is verified by GWT... any idea why?  
+Sandeep Verma  I'd look at the sitemaps indexed URL count more as a metric, since the index status count can include URLs that you don't really care about. Don't blindly follow any metric, think about where it comes from & consider if it's really what you need to focus on.
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